cummeRbund

Package: cummeRbund
Title: Analysis, exploration, manipulation, and visualization of
Cufflinks high-throughput sequencing data.
Version: 2.14.0
Date: 2013-04-22
Author: L. Goff, C. Trapnell, D. Kelley
Description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2,
reshape2, fastcluster, rtracklayer, Gviz
Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
Maintainer: Loyal A. Goff <lgoff@csail.mit.edu>
License: Artistic-2.0
Collate: AllGenerics.R AllClasses.R database-setup.R methods-CuffSet.R
methods-CuffData.R methods-CuffDist.R methods-CuffGeneSet.R
methods-CuffFeatureSet.R methods-CuffGene.R
methods-CuffFeature.R tools.R
LazyLoad: yes
biocViews: HighThroughputSequencing, HighThroughputSequencingData,
RNAseq, RNAseqData, GeneExpression, DifferentialExpression,
Infrastructure, DataImport, DataRepresentation, Visualization,
Bioinformatics, Clustering, MultipleComparisons, QualityControl
NeedsCompilation: no
Packaged: 2016-05-04 04:17:08 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'cummeRbund' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'cummeRbund'
    finding HTML links ... done
    CuffData-class                          html  
    CuffDist-class                          html  
    CuffFeature-class                       html  
    CuffFeatureSet-class                    html  
    CuffGene-class                          html  
    CuffGeneSet-class                       html  
    CuffSet-class                           html  
    JSdist                                  html  
    JSdistFromP                             html  
    JSdistVec                               html  
    MAplot                                  html  
    PINK1                                   html  
    QCplots                                 html  
    addFeatures                             html  
    count                                   html  
    countMatrix                             html  
    csBoxplot                               html  
    csCluster                               html  
    csClusterPlot                           html  
    csDendro                                html  
    csDensity                               html  
    csDistHeat                              html  
    csHeatmap                               html  
    csScatter                               html  
    csSpecificity                           html  
    csVolcano                               html  
    cummeRbund-package                      html  
    diffData                                html  
    dimensionality                          html  
    dispersionPlot                          html  
    distValues                              html  
    exploratory                             html  
    expressionBarplot                       html  
    expressionPlot                          html  
    featureNames                            html  
    features                                html  
    findGene                                html  
    findSimilar                             html  
    fpkm                                    html  
    fpkmMatrix                              html  
    getFeatures                             html  
    getGene                                 html  
    getGeneId                               html  
    getGenes                                html  
    getLevels                               html  
    getRepLevels                            html  
    getSig                                  html  
    getSigTable                             html  
    makeprobs                               html  
    makeprobsvec                            html  
    readCufflinks                           html  
    repFpkm                                 html  
    replicates                              html  
    runInfo                                 html  
    sampleGeneSet                           html  
    sampleIDs                               html  
    samples                                 html  
    shannon.entropy                         html  
    sigMatrix                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cummeRbund)
Making 'packages.html' ... done